Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1a9xa1 | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | All α |
| Hit | d1vkea_ | Hypothetical protein TM1620 | AhpD-like | AhpD-like | All α |
Query <-- 0.803 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:188.40) query 1 dadeevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpsk 60 d1a9xa1 1 ------------------------------------------------------------ 1 query 61 yssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmais 120 d1a9xa1 1 ------------------------------------------------------------ 1 query 121 nqeghivlapgNKSElavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtp 180 :::: d1a9xa1 1 -------evgaTGFD----------------------------------pkvslddpeal 19 query 181 pipeasitkpdyPVLDAILELYVdRDTGADAIVAAG-YDRELVVKTLRMVDTA-EYKRRQ 238 ::::::::::: :::::::::::: :::::::::::::::: :::::: d1a9xa1 20 tkirrelkdagaDRIWYIADAFR-AGLSVDGVFNLTnIDRWFLVQIEELVRLEeKVAEVG 78 query 239 -------------------------YPPGT----------------------kisakgfg 251 ::::: d1a9xa1 79 itglnadflrqlkrkgfadarlaklAGVREaeirklrdqydlhpvykrvdtcaaefatdt 138 query 252 kdrrlpitnrwregh 266 d1a9xa1 139 aymystyeeeceanp 153 FAST alignment (Normalized score: 1.04 Raw score:209.40) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 d1a9xa1 1 ------------------------------------------------------------ 1 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE--------------------------------- 87 d1a9xa1 1 ---------------------------EVGATGFDPKVSLDDPEALTKIRRELKDAGADR 33 query 88 -----------PMFDAYMASLGLTGL-AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSE 135 ::::::::::: :::::::::::::::::::: d1a9xa1 34 IWYIADAFRAGLSVDGVFNLTN----IDRWFLVQIEELVRLEEKVAE------------- 76 query 136 LAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 195 d1a9xa1 77 ------------------------------------------------------------ 77 query 196 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 255 d1a9xa1 77 ------------------------------------------------------------ 77 query 256 LPITNRWREGH------------------------------------------------- 266 d1a9xa1 77 -----------VGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYK 125 query 267 ---------------------------- 267 d1a9xa1 126 RVDTCAAEFATDTAYMYSTYEEECEANP 153 TMalign alignment (TM-score: 0.24 Raw score:64.36) query 1 --------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDA 46 :::::::::: ::: : d1a9xa1 1 EVGATGFDPKVSLD-----DPEALTKIRR-----------------------ELK-D--- 28 query 47 LGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEEN 106 : d1a9xa1 29 -------A---------------------------------------------------- 29 query 107 LQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYK-TSIFRL 165 :::::: ::::::: :::::: d1a9xa1 30 --------------------GADRIW--------------------YIADAFRAGLSVDG 49 query 166 AEWRNRAAAERGQTPPIPEASITK--PDY-PVLDAILELYVDRDT--GADAIVAAGYDRE 220 :: : ::: :::: :: :::::::::: :::: ::: : : d1a9xa1 50 VF--N----------LTN--IDRWFL-VQIEELVRLEEKV-AEVGITGLN--A-----D- 85 query 221 LVVKTLR--MVDTAEYKR-RQYPPGTKISAKGFG-KDRRLPITNRWRE-GH--------- 266 :::::: :::: : : ::: ::::::::::: :: d1a9xa1 86 -FLRQLKRKGFAD-A--RL------------AKLA--GVREAEIRKLRDQYDLHPVYKRV 127 query 267 -------------------------- 267 d1a9xa1 128 DTCAAEFATDTAYMYSTYEEECEANP 153 HHsearch alignment (Probability: 0.03 E-value:0.25) query 197 AILELYVDRDTGADAIVA-AGYDRELVVKTLRMVDTAE 233 :::::::::::::::::: ::::::::::::::::::: d1a9xa1 35 WYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEE 72
Intermediate <-- 0.875 --> HitDALI alignment (Z-score: 3.9 Raw score:234.80) d1a9xa1 1 ---eVGAT----------------gfdpkvsLDDP--EALTKIRRELKDAG-----ADRI 34 :::: :::: :::::::::::::: :::: d1vkea_ 1 kkfvEARRelnekvsrgtlntkrffnldsavYRPGklDVKTKELMGLVASTvlrcdDCIR 60 d1a9xa1 35 WYIADAFRAGLSVDGVFNLTN---------------idRWFLVQIEELVRLEEkvaevgi 79 ::::::::::::::::::::: ::::::::::::::: d1vkea_ 61 YHLVRCVQEGASDEEIFEALDialvvggsiviphlrraVGFLEELREMEKNGE------- 113 d1a9xa1 80 tglnadflrqlkrkgfadarlaklagvreaeirklrdqydlhpvykrvdtcaaefatdta 139 d1vkea_ 114 ------------------------------------------------------------ 114 d1a9xa1 140 ymystyeeeceanp 153 d1vkea_ 114 ----------tisl 117 FAST alignment (Normalized score: 3.26 Raw score:436.50) d1a9xa1 1 EVGATGFDPKVSLDDP-------------------------------------EALTKIR 23 ::::::: d1vkea_ 1 ----------------KKFVEARRELNEKVSRGTLNTKRFFNLDSAVYRPGKLDVKTKEL 44 d1a9xa1 24 RELKDAG--------ADRIWYIADAFRAGLSVDGVFNLTNI-----------DRWFLVQI 64 :::: ::::::::::::::::::::::: :::::::: d1vkea_ 45 MGLV---ASTVLRCDDCIRYHLVRCVQEGASDEEIFEA---LDIALVVGGSIVIPHLRRA 98 d1a9xa1 65 EELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVY 124 :::::::::::: d1vkea_ 99 VGFLEELREMEK------------------------------------------------ 110 d1a9xa1 125 KRVDTCAAEFATDTAYMYSTYEEECEANP------- 153 d1vkea_ 111 -----------------------------NGETISL 117 TMalign alignment (TM-score: 0.32 Raw score:49.22) d1a9xa1 1 EVGATGF--D---------------------PK--VS----LDD-PEALTKIRRELKDAG 30 :::: : : :: :: :::::::::::: :: d1vkea_ 1 ---KKFVEARRELNEKVSRGTLNTKRFFNLD-SAVYRPGKL-DVKTKELMGLVASTV-LR 54 d1a9xa1 31 ADRIWYIA-DA--FR---A---GLS--VDGVFNLTN-IDRWFLVQIEELVRLEEKVAEVG 78 :::::: :: :: : ::: ::::::::: ::::::::::::::::::::::: d1vkea_ 55 --CDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNG 112 d1a9xa1 79 ITGLNADFLRQLKRKGFADARLAKLAG---VREAEIRKLRDQYDLHPVYKRVDTCAAEFA 135 :: d1vkea_ 113 -------------------------ETISL------------------------------ 117 d1a9xa1 136 TDTAYMYSTYEEECEANP 153 d1vkea_ 118 ------------------ 118 HHsearch alignment (Probability: 0.19 E-value:0.01) d1a9xa1 29 AGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLR 88 ::::::::::::::::::::: ::::::::::::::::::: :::::: d1vkea_ 19 LNTKRFFNLDSAVYRPGKLDV-------------KTKELMGLVASTVLRCDDC-IRYHLV 64 d1a9xa1 89 QLKRKGFADARLAKLAG 105 ::::::::::::::::: d1vkea_ 65 RCVQEGASDEEIFEALD 81